The programs on this page can be compiled with optimizations to run on Sun UltraSPARC workstations and servers running the Solaris 2.5.1 operating system.
In some cases, the application requires the Creator 3D graphics system and/or the Sun versions of C, C++, or Fortran compilers. Note that there may also be versions that work on non-UltraSPARC systems. Please check each site for more information on this.
For now, the binaries and other files necessary to produce the optimized code can be found at the sites mentioned below, though some of the programs will also have pre-optimized binaries on our ftp server. Please note that these programs are NOT in the same pre-compiled pkgadd form as the files on the Solaris Freeware Site.
We strongly recommend that you carefully read the installation instructions so that it is clear what hardware and software configurations may be needed to get the best performance. The programs on this page will be periodically updated. Please check back.
Contact the authors at their email addresses or web sites for further information.
The systems currently available are:
BLAST. A tool for matching sequences of genetic information.
Fasta. Programs used to scan a protein or DNA sequence library for similar sequences.
GAMESS. The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
LASSAP. LASSAP is a software package for sequence comparison.
Vis5d. A system for interactive visualization of large 5-D gridded data sets.
Program description:
Basic Local Alignment Search Tool (BLAST) - is a tool for matching
sequences of genetic information.
BLAST performs fast database searching combined with rigorous statistics
for judging the significance of matches. Five BLAST programs search
many different combinations of query and database sequences. The BLAST
algorithm is described in S.F. Altschul, W. Gish, W. Miller, E.W. Myers,
and D.J. Lipman, J. Mol. Biol. 215, 403-10 (1990).
Distribution and Licensing availability:
BLAST binaries, licensing information, documentation and data are
distributed by the National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/.
A distribution of BLAST 1.4.9 optimized for Sun UltraSPARC is included here,
along with a set of binaries. Edit and run the BLAST.run script to rebuild
the binaries.
An UltraSPARC specific version can be found at:
ftp://ftp.sunfreeware.com/pub/freeware/sparc/2.6/ultra/blast.tar.gz
but this may not always be the most up-to-date version. The above file
is over 11 megabytes in .tar.gz form. You will need the
gunzip program found at the main freeware site,
Program description:
The Fasta programs are used to scan a protein or DNA sequence library
for similar sequences.
Distribution availability:
A distribution, including a version optimized for Solaris 2.5.1
UltraSPARC is available from ftp://ftp.virginia.edu/pub/fasta/. See specifically:
ftp://ftp.virginia.edu/pub/fasta/fasta2.shar.Z
ftp://ftp.virginia.edu/pub/fasta/fasta3.shar.Z
The parallel version of fasta is found only in the fasta3.shar.Z file.
However, there are some additional sequence analysis programs (and
documentation) that are found only in the fasta2.shar.Z file, so
users will generally want to download both.
There are no separate ultra-specific files. There is a Makefile.sun
in both distributions. The Makefile.sun in fasta3.shar.Z
has some Ultra specific options.
The author is Bill Pearson and can be contacted at: wrp@virginia.edu.
Licensing information:
Copyright 1988, 1991, 1992, 1993, 1994 1995, by William
R. Pearson and the University of Virginia. All rights
reserved. The FASTA program and documentation may not be sold or
incorporated into a commercial product, in whole or in part,
without written consent of William R. Pearson and the University
of Virginia. For further information regarding permission for
use or reproduction, please contact:
David Hudson
(804) 924-6853
Program description:
The General Atomic and Molecular Electronic Structure System (GAMESS)
is a general ab initio quantum chemistry package. This program is
maintained by the members of the Gordon research group at Iowa State
University.
Distribution availability:
Instructions on how to get a copy of GAMESS are available at the
GAMESS Home Page
http://www.msg.ameslab.gov/GAMESS/GAMESS.html.
Licensing information:
A site license for GAMESS is available at no cost to both academic and
industrial users. You will be asked to print out on paper, sign, and
mail a letter acknowledging the Gordon group's copyright to GAMESS.
This letter also prohibits you from making copies of GAMESS except for
use at your own institution. Please note the distinction between "a
site license at no cost" and terms such as "public domain" or
"freeware".
Program description:
LASSAP is a software package for sequence comparison. It is a programmable,
high performance system that implements all major sequence comparison
algorithms including Fasta, Blast, Smith/Waterman and others. An API
(Application Programming Interface) also allows integration of other
generic pairwise-based algorithms.
LASSAP authors have utilized Sun's Visual Instruction Set (VIS) to speed up
sequence comparison in the Smith/Waterman algorithm.
LASSAP package is written in C and also has a Java graphical interface for
interacting with the 5 programs that make up LASSAP.
Distribution and Licensing availability:
LASSAP binaries, licensing information, documentation and data are
distributed by INRIA, the French National Institute for Research in
Computer Science and Control.
More information and download links can be found at http://alize.inria.fr/.
The UltraSPARC version (Smith/Waterman using VIS) is
available on request. To request a copy, send mail to
lassap@inria.fr.
Program description:
Vis5D is a system for interactive visualization of large 5-D gridded
data sets such as those made by numeric weather models. One can make
isosurfaces, contour line slices, colored slices, volume renderings, etc
of data in a 3-D grid then rotate and animate the image in real time.
There's also a feature for wind/trajectory tracing, a way to make text
anotations for publications, etc.
Distribution availability:
More information, source code and binaries optimized for Sun including
Solaris 2.5.1 and UltraSPARC can be obtained from
http://www.ssec.wisc.edu/~billh/vis5d.html.
Email can be sent to Bill Hibbard at whibbard@macc.wisc.edu .
Licensing information:
Vis5D is distributed under the GNU GENERAL PUBLIC LICENSE Version 1,
February 1989.
BLAST
Fasta
Assistant Provost for Research
University of Virginia
P.O. Box 9025
Charlottesville, VA 22906-9025
Gamess
LASSAP
Vis5D
© Copyright 2001 Steven M. Christensen and Associates, Inc.
This page was last updated on September 26, 2010.